creatininase-product complex

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism

Yoshimoto, T.Tanaka, N.Kanada, N.Inoue, T.Nakajima, Y.Haratake, M.Nakamura, K.T.Xu, Y.Ito, K.

(2004) J Mol Biol 337: 399-416

  • DOI: https://doi.org/10.1016/j.jmb.2004.01.022
  • Primary Citation of Related Structures:  
    1J2T, 1J2U, 1V7Z

  • PubMed Abstract: 

    Creatininase from Pseudomonas putida is a member of the urease-related amidohydrolase superfamily. The crystal structure of the Mn-activated enzyme has been solved by the single isomorphous replacement method at 1.8A resolution. The structures of the native creatininase and the Mn-activated creatininase-creatine complex have been determined by a difference Fourier method at 1.85 A and 1.6 A resolution, respectively. We found the disc-shaped hexamer to be roughly 100 A in diameter and 50 A in thickness and arranged as a trimer of dimers with 32 (D3) point group symmetry. The enzyme is a typical Zn2+ enzyme with a binuclear metal center (metal1 and metal2). Atomic absorption spectrometry and X-ray crystallography revealed that Zn2+ at metal1 (Zn1) was easily replaced with Mn2+ (Mn1). In the case of the Mn-activated enzyme, metal1 (Mn1) has a square-pyramidal geometry bound to three protein ligands of Glu34, Asp45, and His120 and two water molecules. Metal2 (Zn2) has a well-ordered tetrahedral geometry bound to the three protein ligands of His36, Asp45, and Glu183 and a water molecule. The crystal structure of the Mn-activated creatininase-creatine complex, which is the first structure as the enzyme-substrate/inhibitor complex of creatininase, reveals that significant conformation changes occur at the flap (between the alpha5 helix and the alpha6 helix) of the active site and the creatine is accommodated in a hydrophobic pocket consisting of Trp174, Trp154, Tyr121, Phe182, Tyr153, and Gly119. The high-resolution crystal structure of the creatininase-creatine complex enables us to identify two water molecules (Wat1 and Wat2) that are possibly essential for the catalytic mechanism of the enzyme. The structure and proposed catalytic mechanism of the creatininase are different from those of urease-related amidohydrolase superfamily enzymes. We propose a new two-step catalytic mechanism possibly common to creatininases in which the Wat1 acts as the attacking nucleophile in the water-adding step and the Wat2 acts as the catalytic acid in the ring-opening step.

  • Organizational Affiliation

    Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan. yosimoto@net.nagasaki-u.ac.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
creatinine amidohydrolase
A, B, C, D, E
A, B, C, D, E, F
260Pseudomonas sp.Mutation(s): 0 
Find proteins for P83772 (Pseudomonas putida)
Explore P83772 
Go to UniProtKB:  P83772
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83772
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CRN

Download Ideal Coordinates CCD File 
DA [auth D]
JA [auth E]
L [auth A]
PA [auth F]
R [auth B]
DA [auth D],
JA [auth E],
L [auth A],
PA [auth F],
R [auth B],
X [auth C]
C4 H9 N3 O2
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
GA [auth E]
HA [auth E]
AA [auth D],
BA [auth D],
CA [auth D],
GA [auth E],
HA [auth E],
I [auth A],
IA [auth E],
J [auth A],
K [auth A],
MA [auth F],
NA [auth F],
O [auth B],
OA [auth F],
P [auth B],
Q [auth B],
U [auth C],
V [auth C],
W [auth C]
O4 S
Query on ZN

Download Ideal Coordinates CCD File 
FA [auth E]
H [auth A]
LA [auth F]
N [auth B]
T [auth C]
FA [auth E],
H [auth A],
LA [auth F],
N [auth B],
T [auth C],
Z [auth D]
Query on MN

Download Ideal Coordinates CCD File 
EA [auth E]
G [auth A]
KA [auth F]
M [auth B]
S [auth C]
EA [auth E],
G [auth A],
KA [auth F],
M [auth B],
S [auth C],
Y [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.186α = 90
b = 152.211β = 90
c = 167.119γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance